So I have been kicking around a totally insane crackpot theory that pulls together several disparate threads and inconsistencies in Orc lore.

1. Topal the Pilot mentions Orcs in the early/middle Merethic era, before the events of Resdayn and Trinimac becoming Malacath and his Aldmer transforming into Orsimer. This is important because Topal encounters these early Orcs before any other Aldmer have discovered Tamriel, meaning this predates the Velothi exodus, as they had no concept of a land outside Old Aldmeris.
2. The Iron Orcs of Craglorn have a belief system entirely separate from traditional Malacath followers. They worship the stones and mountains (Earth Bones and Elhnofey?) This is highly unique, given they are the only subset of orcs encountered that don't have some variation of Malacath as their patron. Even the Wood Orcs of Valenwood revere Mauloch/Malacath. Iron Orcs, as well, are exceptionally brutal and crude even by Orc standards. Most probably due to their history with the Nedes and Yokudans, which brings me to my next point.
3. Giant Yellow Goblins of Hammerfell. It's always been a matter of some conjecture, but I personally believe these Giant Yellow Goblins were actually early Iron Orcs, venturing south of Craglorn into Hammerfell. In fact, I believe this encounter may have lead to the conflict that would lead to the strife between Iron Orcs, Nedes and Yokudans later.
4. If Iron Orcs could spread all the way to Southern Hammerfell, they could have easily spread into what would become High Rock, and be encountered by Topal the Pilot. This is, of course, conjecture based on conjecture.

So, what I believe, is that Iron Orcs (who were possibly related to Goblins or were an independent species all their own) existed before Malacath/Trinimac. Perhaps Boethiah felt it wasn't enough to just create a new race of ugly elves, but instead merely changed them into an existing species. Over time, the Aldmer-turned-Orsimer proliferated and outnumbered the Osh Ornim (the Iron Orc's name for themselves) until Orsimer culture dominated cultural identity. The true Orcs of Craglorn simultaneously experienced a massive decline as they came into conflict with the Nedes who were in turn in conflict with the Yokudans. In the end, the Nedes of Craglorn were wiped out, the Osh Ornim were forced to defile and profane their sacred beliefs in order to survive, becoming cave-dwelling savages filled with hatred for themselves and everyone else, and the Yokudans became the Redguards and settled Hammerfell.

So there you have it. My insane crackpot theory that Orsimer are not the first orcs. That the Osh Ornim were the first True Orcs, but the chaos of the middle to late Merethic era saw their culture and identity eclipsed by the more numerous and culturally advanced Orsimer.

It's probably wrong, but I rather like the idea that Orcs have a bit more depth to them than literal Malacath Poop Servants.